Replication error deficient and proficient colorectal cancer gene expression differences caused by 3′UTR polyT sequence deletions

Abstract

Replication error deficient (RER+) colorectal cancers are a distinct subset of colorectal cancers, characterized by inactivation of the DNA mismatch repair system. These cancers are typically pseudodiploid, accumulate mutations in repetitive sequences as a result of their mismatch repair deficiency, and have distinct pathologies. Regulatory sequences controlling all aspects of mRNA processing, especially including message stability, are found in the 3′UTR sequence of most genes. The relevant sequences are typically A/U-rich elements or U repeats. Microarray analysis of 14 RER+ (deficient) and 16 RER− (proficient) colorectal cancer cell lines confirms a striking difference in expression profiles. Analysis of the incidence of mononucleotide repeat sequences in the 3′UTRs, 5′UTRs, and coding sequences of those genes most differentially expressed in RER+ versus RER− cell lines has shown that much of this differential expression can be explained by the occurrence of a massive enrichment of genes with 3′UTR T repeats longer than 11 base pairs in the most differentially expressed genes. This enrichment was confirmed by analysis of two published consensus sets of RER differentially expressed probesets for a large number of primary colorectal cancers. Sequence analysis of the 3′UTRs of a selection of the most differentially expressed genes shows that they all contain deletions in these repeats in all RER+ cell lines studied. These data strongly imply that deregulation of mRNA stability through accumulation of mutations in repetitive regulatory 3′UTR sequences underlies the striking difference in expression profiles between RER+ and RER− colorectal cancers.A pproximately 15% of sporadic colorectal cancers (CRCs) are microsatellite unstable (MSI+) as a result of inactivation of one of the components of the DNA mismatch repair system (1). This is mostly because of a combination of epigenetic silencing or mutation, coupled with loss of heterozygosity, of MLH1 and less frequently MSH2 or MSH6 (2, 3). As a result, such tumors are replication error deficient (RER+), which leads to the accumulation of insertion/deletion mutations in mono-, di-, tri-, and tetranucleotide repeats throughout the genome, probably because of DNA polymerase slippage during replication (4, 5).RER+ tumors have distinct clinico-pathologic and genetic profiles in comparison with microsatellite stable/replication proficient tumors (MSI−/RER−). These tumors tend to be right sided (proximal), poorly differentiated with mucinous histology, and have a more favorable prognosis (6-8). In addition, they mostly have a near diploid or pseudodiploid karyotype; RER− tumors are mostly chromosomally unstable and have aneuploid karyotypes (9, 10). The underlying genetic instability in RER+ tumors results in a genetic profile that is distinct from RER− tumors and is characterized by mutation of "susceptible" genes containing repeat sequences within their protein coding regions. For example, although the TGF signaling pathway is commonly disrupted in CRC, RER+ tumors tend...

Cancer Cell Lines for Drug Discovery and Development

“…This makes cell line studies on large numbers of drug combinations quite feasible. Many cell lines have now already been exhaustively characterized (8,12,13,15,16). They represent the spectrum of mutations found in cancers, have similar patterns of chromosomal gains and losses, methylation and mRNA expression, and show no evidence of genetic changes in major driver mutations on longterm in vitro cultivation.…”

“…As such, it provides a good example of how well cell lines reflect the wide spectrum of subtypes of a particular cancer with respect to mRNA expression profiles (13) and common mutations (14). For colorectal cancer, these include mutations in the genes APC, TP53, CTNNB1, BRAF, PIK3CA, and FBXW7, and the mismatch repair genes, mainly MLH1 and MSH2.…”

Colorectal Cancer Cell Lines Are Representative Models of the Main Molecular Subtypes of Primary Cancer

“…UTR mutations can impact on RNA splicing, stability, or translation as previously highlighted for MSI-H colorectal cancer (44). In the comparison of gene mutation profiles, we chose to exclude silent mutations (other than those affecting splice sites), although some of these may similarly have functional consequences (45).…”

EGF signalling in epithelial carcinoma cells utilizes preformed receptor homoclusters, with larger heteroclusters post activation

“…Human epithelial cell line SW620 was selected from an extensive colorectal carcinoma library for its undetectable EGFR expression as quantified by DNA microarray 42 (Supplementary Fig. 1) and western blot (Fig.…”

“…We screened all ~100 colorectal cancer cell lines from the Cancer and Immunogenetics Laboratory (Weatherall Institute of Molecular Medicine, Oxford University, U.K.) for EGFR mRNA using available microarray data 42 (Supplementary Fig. 1) and selected three preliminary lines (SW620, COLO320HSR and COLO741) on the basis of negligible native EGFR expression levels prior focussing on SW620 (COLO741 was found to be a melanoma line and COLO320HSR exhibited transfection instability).…”